18-1916607-A-G

Position:

• chr18-1916607-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661994.1(ENSG00000266602):​n.500+44676A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (28810 hom., cov: 19)
• Consequence: ENST00000661994.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371958	XR_001753320.2	n.232+5556T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661994.1	n.500+44676A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.640 AC: 88426 AN: 138134 Hom.: 28780 Cov.: 19

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.594

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.663

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.640 AC: 88486 AN: 138206 Hom.: 28810 Cov.: 19 AF XY: 0.640 AC XY: 42575 AN XY: 66514

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.667

Alfa AF: 0.603 Hom.: 26480

Bravo AF: 0.658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9949006; hg19: chr18-1916608;